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Open Access Research article

An interaction-motif-based scoring function for protein-ligand docking

Zhong-Ru Xie12 and Ming-Jing Hwang12*

Author Affiliations

1 Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan

2 Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan

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BMC Bioinformatics 2010, 11:298  doi:10.1186/1471-2105-11-298

Published: 2 June 2010

Abstract

Background

A good scoring function is essential for molecular docking computations. In conventional scoring functions, energy terms modeling pairwise interactions are cumulatively summed, and the best docking solution is selected. Here, we propose to transform protein-ligand interactions into three-dimensional geometric networks, from which recurring network substructures, or network motifs, are selected and used to provide probability-ranked interaction templates with which to score docking solutions.

Results

A novel scoring function for protein-ligand docking, MotifScore, was developed. It is non-energy-based, and docking is, instead, scored by counting the occurrences of motifs of protein-ligand interaction networks constructed using structures of protein-ligand complexes. MotifScore has been tested on a benchmark set established by others to assess its ability to identify near-native complex conformations among a set of decoys. In this benchmark test, 84% of the highest-scored docking conformations had root-mean-square deviations (rmsds) below 2.0 Å from the native conformation, which is comparable with the best of several energy-based docking scoring functions. Many of the top motifs, which comprise a multitude of chemical groups that interact simultaneously and make a highly significant contribution to MotifScore, capture recurrent interacting patterns beyond pairwise interactions.

Conclusions

While providing quite good docking scores, MotifScore is quite different from conventional energy-based functions. MotifScore thus represents a new, network-based approach for exploring problems associated with molecular docking.